Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007534.1 Hibiscus syriacus cultivar Beakdansim tig00021057_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 86642
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:26145 original size:3 final size:3
Alignment explanation
Indices: 26139--26204 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
26129 TTAGATAAAT
26139 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26187 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
26205 CTCTATCAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27068 original size:2 final size:2
Alignment explanation
Indices: 27061--27088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27051 TGTGAATCTC
27061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27089 GGATATACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31809 original size:30 final size:30
Alignment explanation
Indices: 31768--33336 Score: 1621
Period size: 30 Copynumber: 52.4 Consensus size: 30
31758 GTGAGCCGGT
* * *
31768 TCCATATAAGTACGAGTCGCCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * ** ** * *
31798 ACCATACAAGTATAAGTCGTCACAACCTCT
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
31828 TCCATACAAGTACAAGTCACCTCCT-C-CC
1 TCCATACAAGTACAAGTCACCACCTCCACC
**
31856 -CC--AC-CTTACAAGTCACCA-CTACCACC
1 TCCATACAAGTACAAGTCACCACCT-CCACC
* * *
31882 TCCGTACAAGTACGAGTCGCCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
31912 TCCATACAAATATAAGTCACCAACACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
31942 TCCATATACGTACGAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* *
31972 TCCATATAAGTACAAGTCACCACCACCACCTCC
1 TCCATACAAGTACAAGTCACCACCTCCA---CC
* ** ** *
32005 TCCATACATGTATGAGTCACCACAACCACT
1 TCCATACAAGTACAAGTCACCACCTCCACC
* *
32035 TCCATACAAGTACGAGTCA-CATCCTCCTCC
1 TCCATACAAGTACAAGTCACCA-CCTCCACC
* * *
32065 TCCGTACAAGTACAAGTCACCACCACCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
32095 TCCGTATAAGTACGAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * *
32125 TCCATACAAGTATAAGTCACCACCACCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* **
32155 TCCGTACAAGTATGAGTCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * *
32185 TCCATACAAGTACAAGTCATCAACACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* *
32215 TCCGTACAAGTACGAGTCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
32245 TCCATACAAGTACAAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
32275 TCTATACAAGTACGAGTCACCTCCTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
32305 TACATACAAGTATAAGTCACCACCACCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* *
32335 TCCGTACAAGTACGAA-TCCCCTA-CTCCACC
1 TCCATACAAGTAC-AAGTCACC-ACCTCCACC
* * * *
32365 TCCATACAAGTATAAGTCACCACCACCTCT
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
32395 TTCGTACAAGTACAAGTCACCTCCTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
32425 TCCCTATAAGTACAAGTCTCCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
32455 TCCGTACAAGTACGAGTCACCTCCTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
32485 TCCATACAAGTACAAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
** *
32515 TCCATACAAGTATGAGTCTCCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
32545 TCCATACAAGTACAAGCCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* **
32575 TCCGTACAAGTATGAGTCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
32605 TCCATACAAGTACAAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * *
32635 TCCATACAAGTACGAGTCACCTCCTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
32665 TCCATACAAGTACAAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
** *
32695 TCCATACAAGTATGAGTCTCCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
32725 TCCATATAAGTACAAGTCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* **
32755 TCCGTACAAGTATGAGTCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* *
32785 TCCATACAAGTACAAGTCACTACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
** * * *
32815 TCCATACAAGTATGAGTCACCTCCACCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* *
32845 TCCTTACAAGTACAAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * *
32875 TCCGTATAAGTACGAA-TCACCACCTTCACA
1 TCCATACAAGTAC-AAGTCACCACCTCCACC
* * *
32905 TCAATACAAGTATAAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
** * *
32935 TCCATACAAGTATGAGTCACCTCCTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * *
32965 TCCTTACAAGTACAAGTCACAACCTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
**
32995 TCCATACAAGTATGAGTCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
33025 TCCATACAAGTACAAGTCACCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
33055 TCCATACAAGTACGAGTCACCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * *
33085 TCCATACAAGTATAAGTCGCCACCACCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
** * *
33115 TCCATACAAGTATGAGTCACCTCCTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * *
33145 TCCGTACAAGTACAAGTCACCACGTCCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * *
33175 TCCGTACAAGTACGAGTCGCCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
*
33205 TCCATACAAGTACAAGTCGCCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* *
33235 TCCATACAAGTACAAGTCACCACCACCTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * **
33265 TACATACAAGTACGAGTTGCCACCTCCACC
1 TCCATACAAGTACAAGTCACCACCTCCACC
* * * **
33295 ACCATACAAGTACGAGTCACCACCACTTCC
1 TCCATACAAGTACAAGTCACCACCTCCACC
33325 TCCATACAAGTA
1 TCCATACAAGTA
33337 TGAATCACCT
Statistics
Matches: 1272, Mismatches: 248, Indels: 38
0.82 0.16 0.02
Matches are distributed among these distances:
23 2 0.00
24 11 0.01
25 3 0.00
26 2 0.00
27 4 0.00
28 1 0.00
29 10 0.01
30 1205 0.95
31 9 0.01
33 25 0.02
ACGTcount: A:0.31, C:0.41, G:0.09, T:0.19
Consensus pattern (30 bp):
TCCATACAAGTACAAGTCACCACCTCCACC
Found at i:32163 original size:120 final size:120
Alignment explanation
Indices: 31866--33336 Score: 1823
Period size: 120 Copynumber: 12.2 Consensus size: 120
31856 CCACCTTACA
* * * * * **
31866 AGTCACCA-CTACCACCTCCGTACAAGTACGAGTCGCCACCTCCACCTCCATACAAATATAAGTC
1 AGTCACCACCT-CCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTC
* * * * * * *
31930 ACCAACACCACCTCCATATACGTACGAGTCACCACCACCACCTCCATATAAGTACA
65 ACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * ** * *
31986 AGTCACCACCACCACCTCCTCCATACATGTATGAGTCACCACAACCACTTCCATACAAGTACGAG
1 AGTCACCACCTCCA---CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAG
* * * * *
32051 TCA-CATCCTCCTCCTCCGTACAAGTACAAGTCACCACCACCTCCTCCGTATAAGTACG
63 TCACCA-CCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * * * *
32109 AGTCACCACCACCACCTCCATACAAGTATAAGTCACCACCACCTCCTCCGTACAAGTATGAGTCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* * *
32174 CCACCTCCACCTCCATACAAGTACAAGTCATCAACACCACCTCCGTACAAGTACG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
*
32229 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCTATACAAGTACGAGTCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* * * * * *
32294 CCTCCTCCTCCTACATACAAGTATAAGTCACCACCACCTCCTCCGTACAAGTACG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * * * * * * *
32349 AATCCCCTA-CTCCACCTCCATACAAGTATAAGTCACCACCACCTCTTTCGTACAAGTACAAGTC
1 AGTCACC-ACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTC
* * * * * *
32413 ACCTCCTCCTCCTCCCTATAAGTACAAGTCTCCACCACCACCTCCGTACAAGTACG
65 ACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * * *
32469 AGTCACCTCCTCCTCCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTATGAGTCT
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* * * *
32534 CCACCTCCACCTCCATACAAGTACAAGCCACCACCTCCACCTCCGTACAAGTATG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
32589 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* * *
32654 CCTCCTCCTCCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTATG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * * * *
32709 AGTCTCCACCTCCACCTCCATATAAGTACAAGTCACCACCTCCACCTCCGTACAAGTATGAGTCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* *
32774 CCACCTCCACCTCCATACAAGTACAAGTCACTACCACCACCTCCATACAAGTATG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * * * * * *
32829 AGTCACCTCCACCTCCTCCTTACAAGTACAAGTCACCACCACCACCTCCGTATAAGTACGAATCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* * * * *
32894 CCACCTTCACATCAATACAAGTATAAGTCACCACCACCACCTCCATACAAGTATG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * * * * * *
32949 AGTCACCTCCTCCTCCTCCTTACAAGTACAAGTCACAACCTCCTCCTCCATACAAGTATGAGTCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
33014 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * *
33069 AGTCACCACCTCCACCTCCATACAAGTATAAGTCGCCACCACCACCTCCATACAAGTATGAGTCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* * * ** * *
33134 CCTCCTCCTCCTCCGTACAAGTACAAGTCACCACGTCCTCCTCCGTACAAGTACG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* * * *
33189 AGTCGCCACCTCCACCTCCATACAAGTACAAGTCGCCACCTCCACCTCCATACAAGTACAAGTCA
1 AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
* * * * ** * *
33254 CCACCACCTCCTACATACAAGTACGAGTTGCCACCTCCACCACCATACAAGTACG
66 CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
* **
33309 AGTCACCACCACTTCCTCCATACAAGTA
1 AGTCACCACCTCCACCTCCATACAAGTA
33337 TGAATCACCT
Statistics
Matches: 1181, Mismatches: 162, Indels: 16
0.87 0.12 0.01
Matches are distributed among these distances:
120 1078 0.91
121 4 0.00
122 2 0.00
123 97 0.08
ACGTcount: A:0.31, C:0.41, G:0.09, T:0.19
Consensus pattern (120 bp):
AGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAGTCA
CCACCTCCACCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACG
Found at i:33062 original size:24 final size:24
Alignment explanation
Indices: 33035--33082 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
33025 TCCATACAAG
33035 TACAAGTCACCA-CCACCACCTCCA
1 TACAAGT-ACCAGCCACCACCTCCA
* *
33059 TACAAGTACGAGTCACCACCTCCA
1 TACAAGTACCAGCCACCACCTCCA
33083 CCTCCATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.33, C:0.44, G:0.08, T:0.15
Consensus pattern (24 bp):
TACAAGTACCAGCCACCACCTCCA
Found at i:34569 original size:60 final size:59
Alignment explanation
Indices: 34423--34569 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 59
34413 AACATAATGA
* * * * *
34423 ATAGTCAGGTGACTATTTTGTAACTTTTAATAGTCGATGGACTTAACAAAGCACCATTTT
1 ATAGTCAGGAGACCA-TTTGTAACTTTTAATACTCGATGGACTTAACAAAGCACCACTCT
* * * **
34483 ATAGTTA-GAGGACCATTATGTAACTTTTAATACTTGATGGACTTAATAAAGCAGTACTCT
1 ATAGTCAGGA-GACCATT-TGTAACTTTTAATACTCGATGGACTTAACAAAGCACCACTCT
*
34543 ATAGTCAGGAGACGATTTGTATACTTT
1 ATAGTCAGGAGACCATTTGTA-ACTTT
34570 ACCCTAAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
59 7 0.10
60 62 0.87
61 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (59 bp):
ATAGTCAGGAGACCATTTGTAACTTTTAATACTCGATGGACTTAACAAAGCACCACTCT
Found at i:37299 original size:65 final size:65
Alignment explanation
Indices: 37139--37299 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 65
37129 TTGTTTAAGG
* * * ** *
37139 TGCATCGATGCACATGCAGTGCATCGATGCA--TGAATTTAAATAGAAAACATCGAATGGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCCA-TTAAATAGAAAACATCGAATAGGATTT
37202 A
65 A
* *
37203 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCCATTAAATA-CAAACATTGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCCATTAAATAGAAAACATCGAATAGGATTTA
*
37267 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
37300 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 59 0.70
65 22 0.26
66 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCTCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:38897 original size:25 final size:25
Alignment explanation
Indices: 38863--38922 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
38853 GAGTAGAGGG
38863 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
38888 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
38913 TCTACGCGGT
1 TCTACGCGGT
38923 ACACATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.28
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:40517 original size:21 final size:21
Alignment explanation
Indices: 40492--40540 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
40482 ATTACAGTAT
*
40492 TGATGTGCCAGTTCACGGTGA
1 TGATGTGCCAGTCCACGGTGA
***
40513 TGATGTGGTGGTCCACGGTGA
1 TGATGTGCCAGTCCACGGTGA
40534 TGATGTG
1 TGATGTG
40541 GTGGTCCACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.39, T:0.31
Consensus pattern (21 bp):
TGATGTGCCAGTCCACGGTGA
Found at i:40541 original size:21 final size:21
Alignment explanation
Indices: 40505--40553 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
40495 TGTGCCAGTT
40505 CACGGTGATGATGTGGTGGTC
1 CACGGTGATGATGTGGTGGTC
40526 CACGGTGATGATGTGGTGGTC
1 CACGGTGATGATGTGGTGGTC
40547 CACGGTG
1 CACGGTG
40554 TTGACATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (21 bp):
CACGGTGATGATGTGGTGGTC
Found at i:51810 original size:2 final size:2
Alignment explanation
Indices: 51803--51842 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
51793 AAATTAATCA
51803 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51843 ATTTTCGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54074 original size:19 final size:19
Alignment explanation
Indices: 54050--54111 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
54040 TGAGTTATAA
54050 TAAAATATAATTTTTTTAT
1 TAAAATATAATTTTTTTAT
*
54069 TAAAATATACTTTTTTTAT
1 TAAAATATAATTTTTTTAT
54088 TAAAATATAA-TTTTTTAT
1 TAAAATATAATTTTTTTAT
54106 TAAAAT
1 TAAAAT
54112 TTATCATATC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TAAAATATAATTTTTTTAT
Found at i:59772 original size:2 final size:2
Alignment explanation
Indices: 59765--59789 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59755 CCCTTTTGCC
59765 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
59790 TGCTATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63383 original size:1 final size:1
Alignment explanation
Indices: 63377--63410 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
63367 TGAAATATAT
63377 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
63411 TCCTTTCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:71953 original size:20 final size:20
Alignment explanation
Indices: 71930--71983 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
71920 CTTCTTAATA
71930 GTTCCAGAACCTTCTATGAT
1 GTTCCAGAACCTTCTATGAT
* * * * * *
71950 GTTCTAAAATCTTTTTTTAT
1 GTTCCAGAACCTTCTATGAT
71970 GTTCCAGAACCTTC
1 GTTCCAGAACCTTC
71984 CACAATGTTC
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (20 bp):
GTTCCAGAACCTTCTATGAT
Found at i:72012 original size:20 final size:21
Alignment explanation
Indices: 71989--72028 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
71979 CCTTCCACAA
*
71989 TGTTCTAGAATATTC-AAAGG
1 TGTTCCAGAATATTCTAAAGG
72009 TGTTCCAGAATATTCTAAAG
1 TGTTCCAGAATATTCTAAAG
72029 TATTCTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
TGTTCCAGAATATTCTAAAGG
Found at i:76687 original size:52 final size:51
Alignment explanation
Indices: 76554--76731 Score: 275
Period size: 51 Copynumber: 3.5 Consensus size: 51
76544 TGATAAGTCT
* * * *
76554 GCTCCCTATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAATGTGTCC
**
76605 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAT-AAATGTGTCC
*
76657 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAATGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAATGTGTCC
*
76708 GCTCCCTATTGCTTCAGAGAGTAT
1 GCTCCCTATTCCTTCAGAGAGTAT
76732 GGAAATCAAA
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
51 69 0.59
52 47 0.41
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAATGTGTCC
Found at i:76768 original size:54 final size:54
Alignment explanation
Indices: 76726--76969 Score: 380
Period size: 54 Copynumber: 4.5 Consensus size: 54
76716 TTGCTTCAGA
* * * *
76726 GAGTATGGAAATCAAACGTCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * * * *
76780 GGGTATGGAACTTGAACATATTCTTCTTACGGATTTGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
76834 GAGTATGGAACTCGAGCATCTTCTTTTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
76888 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTTCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
76942 GAGTATGGAACTCGAACATCTTCTTCTT
1 GAGTATGGAACTCGAACATCTTCTTCTT
76970 TACCACTTTA
Statistics
Matches: 171, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 171 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.37
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:77393 original size:37 final size:37
Alignment explanation
Indices: 77342--77465 Score: 151
Period size: 37 Copynumber: 3.4 Consensus size: 37
77332 TTACTCCAAC
* * * *
77342 ACTCTTCCGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
77379 ACTCTTCGGTGAAGGCTTAAGATGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
* * * *
77415 ACTCTTTGGTGAAGGCTCAAATTGGATTTGCTTCATT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
77452 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
77466 ACTTGGCTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
36 31 0.41
37 45 0.59
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:78904 original size:125 final size:125
Alignment explanation
Indices: 78699--78924 Score: 371
Period size: 125 Copynumber: 1.8 Consensus size: 125
78689 TGATACGGGC
* * *
78699 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTGGTCTGAATCTT
1 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTCGTCCGAATCAT
* ** *
78764 GTCATTTCATCATGATGTGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGAGT
66 GTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGAGT
*
78824 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAATGCCTTCTTCGTCCGAATCAT
1 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTCGTCCGAATCAT
*
78889 GTCATCTCAAAATGATGGGGGTTGAGTCATGCCCCA
66 GTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCA
78925 GTATGGGTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 92 1.00
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (125 bp):
CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTCGTCCGAATCAT
GTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGAGT
Found at i:82363 original size:72 final size:72
Alignment explanation
Indices: 82246--82396 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
82236 CCCCTAACAG
*
82246 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACTCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
82311 TTCATCT
66 TTCATAT
* *
82318 GTTCTTGATCATTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
82383 TTCATAT
66 TTCATAT
*
82390 TTTCTTG
1 GTTCTTG
82397 TATAATAGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.37
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:83152 original size:55 final size:55
Alignment explanation
Indices: 83081--83188 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 55
83071 TGTGGATCAG
* *
83081 TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAATCGT
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATCGAATGTCCTTCTTCATGAATCGT
* * *
83136 TCTTCACTCAGGTTCAAATTTCTTCATTCGTCGAATGTTCTTCTTCATGAATC
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATCGAATGTCCTTCTTCATGAATC
83189 ATCTGAATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (55 bp):
TCTTCAATCAGGTTCAAATTTCTTCATTCATCGAATGTCCTTCTTCATGAATCGT
Done.